[gmx-users] WHAM
João Henriques
joao.m.a.henriques at gmail.com
Mon Dec 18 09:14:10 CET 2017
This has nothing to do with your initial question, but I there are a few
misconceptions in your last email that you should be aware of.
First, you don't need "special computers" to run or compile gromacs. It
helps to have multiple compute nodes at your disposal, but it isn't a
requirement *per se*. Also, you don't need to be root to compile your own
gromacs installation. You can indeed install your own gromacs version on
the cluster you use to run your simulations.
Finally, version 2018 is still a beta testing version, so it's probably not
a good idea to use it until it's released as a stable version.
P.S.: Justin does a lot more than the average mortal, specially when it
comes to MD simulations and Gromacs. However, no one ever knows everything.
Cheers,
J
On Mon, Dec 18, 2017 at 8:57 AM, rose rahmani <rose.rhmn93 at gmail.com> wrote:
> Dear Justin,I don't have special computers to be compatible with these
> softwares and run complex calculations.So i have to connect to some
> computers which is not mine and the old version is installed there.i can't
> update them because i'm just a normal user and not a root one! So there are
> two choices; not using GROMACS at all OR be convinced with the old
> versions. i choose latter!
> WHO don't like an upgraded software sir?! you are not talking with a
> headstrong person ;) i like to use V.2018 but it's not possible for me, i
> hope you understand me.💜Just this!
> You are talking with 3 months experienced student without any experience in
> any similar simulation software before!
>
> I agree with you Alex he is a modest person ;)
> I understand sometimes it's not possible to say what the problem exactly
> is, but i ask to know if you had these problems before how did you solve it
> in your system, yes maybe it couldn't be the right answer for another's
> system but maybe a clue for someone!
>
> You have helped me many times and i really appreciate you for your
> attentions and kindness
>
> Thank you again dear Justin and Alex
> Best regards
>
> -Rose
>
> On Mon, Dec 18, 2017 at 12:52 AM, Alex <nedomacho at gmail.com> wrote:
>
> > Rose,
> >
> > Although in my opinion Justin does know everything, the problem is with
> > your question. You've posted the same thing over and over (and over), and
> > noone replied -- this could be an indicator that people simply have
> nothing
> > to say. We don't know anything about your system, we don't know whether
> it
> > is stable, what is its dynamics, etc, etc. On top of this, you are using
> a
> > very outdated Gromacs version.
> >
> > From my own experience with all versions above 5.0.x, pull in Gromacs
> does
> > work well, as long as your system behaves as expected without pulling,
> and,
> > once that has been confirmed, you use a properly selected set of pull
> > parameters. There are basic procedures for checking your system _prior
> to_
> > production simulations involving external stimuli (fields, pulling, etc)
> --
> > please follow them. And please, Please be mindful of what this message
> > board is, and especially of what it is not.
> >
> > Good luck!
> >
> > Alex
> >
> >
> >
> > On 12/17/2017 1:44 PM, Justin Lemkul wrote:
> >
> >>
> >>
> >> On 12/17/17 3:39 PM, Rose wrote:
> >>
> >>> Why you don't answer me?is there anything wrong in my question?
> >>>
> >>
> >> Contrary to popular opinion, I don't know everything :) If I don't reply
> >> to a question, it is because I have nothing useful to contribute.
> >>
> >> But since you asked, diagnosing what appears to be buggy behavior in
> >> wildly outdated (and unsupported, as I warned you) versions of the code
> is
> >> not a wise use of time. Upgrade to the latest version and try again.
> >>
> >> -Justin
> >>
> >> Thank you
> >>>
> >>> Sent from my iPhone
> >>>
> >>> On Dec 17, 2017, at 17:36, rose rahmani <rose.rhmn93 at gmail.com> wrote:
> >>>>
> >>>> Hi,
> >>>>
> >>>> I try to use umbrella sampling for calculating PMF. i change distance
> >>>> between protein and ZNS nanosheet. I use gomacsV4.5.4
> >>>>
> >>>> after minimization and equilibration. i use:
> >>>>
> >>>> grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr
> >>>> this is md_pull.mdp:
> >>>> integrator = md
> >>>> dt = 0.002
> >>>> nsteps = 1000000
> >>>> nstxout = 5000
> >>>> nstvout = 5000
> >>>> nstfout = 500
> >>>> nstlog = 500
> >>>> nstenergy = 1000
> >>>> nstxtcout = 1000
> >>>> nstlist = 10
> >>>> rlist = 1.5
> >>>> coulombtype = pme
> >>>> rcoulomb = 1.5
> >>>> vdwtype = Switch
> >>>> rvdw_switch = 1.0
> >>>> rvdw = 1.2
> >>>> pcoupl = no
> >>>> gen_vel = no
> >>>> constraints = h-bonds
> >>>> ns_type = grid
> >>>> pbc = xy
> >>>> freezegrps = WAL ZnS
> >>>> freezedim = Y Y Y Y Y Y
> >>>> energygrp-excl = WAL WAL ZnS ZnS
> >>>> energygrps = SOL WAL ZnS Protein NA CL
> >>>> nwall = 2
> >>>> wall-atomtype = C C
> >>>> wall-type = 9-3
> >>>> wall-density = 150 150
> >>>> wall-ewald-zfac = 3
> >>>> ewald-geometry = 3dc
> >>>> fourierspacing = 0.12
> >>>> tcoupl = v-rescale
> >>>> tc-grps = System
> >>>> tau-t = 0.1
> >>>> ref-t = 300
> >>>> ; Pull code
> >>>> pull = umbrella
> >>>> pull_ngroups = 1
> >>>> pull_group0 = ZnS
> >>>> pull_group1 = Protein
> >>>> pull_geometry = direction
> >>>> pull_vec1 = 0 0 1
> >>>> pull_dim = N N Y
> >>>> pull_rate1 = -0.01
> >>>> pull_k1 = 5000
> >>>> pull_start = yes
> >>>> pull_nstxout = 50
> >>>>
> >>>> then: mdrun -s pull.tpr
> >>>> then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep
> >>>>
> >>>> i got 1000 configuration, i selected 27 of them and foe each of them i
> >>>> run md_umbrella.mdp
> >>>>
> >>>> for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p
> >>>> topol.top -n index.ndx -o umbrella0.tpr and then:
> >>>> mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px
> pullx-umbrella0.xvg
> >>>>
> >>>> .This is md_umbrella.mdp file:
> >>>>
> >>>> ntegrator = md
> >>>> dt = 0.002
> >>>> nsteps = 2000000
> >>>> nstxout = 5000
> >>>> nstvout = 5000
> >>>> nstfout = 500
> >>>> nstlog = 500
> >>>> nstenergy = 1000
> >>>> nstxtcout = 1000
> >>>> nstlist = 10
> >>>> rlist = 1.5
> >>>> coulombtype = pme
> >>>> rcoulomb = 1.5
> >>>> vdwtype = Switch
> >>>> rvdw_switch = 1.0
> >>>> rvdw = 1.2
> >>>> pcoupl = no
> >>>> gen_vel = no
> >>>> constraints = h-bonds
> >>>> ns_type = grid
> >>>> pbc = xy
> >>>> freezegrps = WAL ZnS
> >>>> freezedim = Y Y Y Y Y Y
> >>>> energygrp-excl = WAL WAL ZnS ZnS
> >>>> energygrps = SOL WAL ZnS Protein NA CL
> >>>> nwall = 2
> >>>> wall-atomtype = C C
> >>>> wall-type = 9-3
> >>>> wall-density = 150 150
> >>>> wall-ewald-zfac = 3
> >>>> ewald-geometry = 3dc
> >>>> fourierspacing = 0.12
> >>>> tcoupl = v-rescale
> >>>> tc-grps = System
> >>>> tau-t = 0.1
> >>>> ref-t = 300
> >>>>
> >>>> pull = umbrella
> >>>> pull_ngroups = 1
> >>>> pull_group0 = ZnS
> >>>> pull_group1 = Protein
> >>>> pull_geometry = direction
> >>>> pull_vec1 = 0 0 1
> >>>> pull_dim = N N Y
> >>>> pull_rate1 = 0.0 ; 1 nm per ns
> >>>> pull_k1 = 5000
> >>>> pull_start = yes
> >>>> pull_nstxout = 50
> >>>> ...........................................................
> >>>>
> >>>> then i use :
> >>>> wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
> >>>>
> >>>> i get histo.xvg and profile.xvg file but the profile.xvg contains nan
> >>>> vavlue. i don't know why?
> >>>>
> >>>> # This file was created Wed Dec 13 14:54:35 2017
> >>>> # by the following command:
> >>>> # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
> >>>> #
> >>>> # g_wham is part of G R O M A C S:
> >>>> #
> >>>> # GROwing Monsters And Cloning Shrimps
> >>>> #
> >>>> @ title "Umbrella potential"
> >>>> @ xaxis label "z"
> >>>> @ yaxis label "E (kcal mol\S-1\N)"
> >>>> @TYPE xy
> >>>> 5.723834e-01 -nan
> >>>> 6.714198e-01 -nan
> >>>> 7.704562e-01 -nan
> >>>> 8.694925e-01 -nan
> >>>> 9.685289e-01 -nan
> >>>> 1.067565e+00 -nan
> >>>> 1.166602e+00 -nan
> >>>> 1.265638e+00 -nan
> >>>> .
> >>>> .
> >>>> .
> >>>> .
> >>>>
> >>>> Would you please help me? i have not encounter this problem before
> >>>> and also i want protein get closer to ZnS sheet during pulling in just
> >>>> Z direction and straightforward to sheet( like one straight line to
> sheet),
> >>>> is this suitable md_pull.mdp file for this approach? and what about
> time?is
> >>>> 4nS suitable for each window?is it possible at all?
> >>>> Would you please help me?
> >>>>
> >>>> Best regards
> >>>> Rose
> >>>>
> >>>
> >>
> > --
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